Hi Andreas:

As far as I know, the complete command is:

recon-all -s subjid -skullstrip -no-wsgcaatlas -wsthresh 35 -clean-bm

Sincerely,

Gonzalo Rojas Costa Laboratory of Medical Imaging Processing Department of Radiology Clínica Las Condes Santiago Chile

Date: Fri, 26 Mar 2010 11:07:01 +0100 From: Andreas Berger andreas.berger.01@gmail.com Subject: [Freesurfer] changing watershed threshold has no effect To: freesurfer@nmr.mgh.harvard.edu Message-ID: 68f948a91003260307g4fee4b69s9c04624544df29a1@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"

hello freesurfers,

we are having a problem with insufficient skull stripping, in 66 out of 200 subjects this affects the pial surface, as can be seen in the attached screenshot1. since the problem is somewhat generalized in location, i tried to change the watershed threshold as suggested by the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean -wsthresh n), but even 0 seems to have no effect (it looks different, but not less skull), see screenshot2. am i doing it wrong?